Loading CPTAC data generates many "gene" records about datahub

[jjgao]

https://github.com/cBioPortal/cbioportal/issues/6309

[pieterlukasse]

@jjgao @zheins @sheridancbio

[pieterlukasse]

Just for the record:

Here an example of a "protein" vs one of its isoforms(?) :

Here is how the isoform(?) is displayed in oncoprint, as "protein upregulation":

[jjgao]

cc'ing @pambot on this.

PHOSPHOPROTEIN and SORBS1_pT72 are definitely hacks we should solve. Ideally, we should be able to pull out SORBS1_pT72 when querying SORBS1. Now we have the generic_entity table. Maybe we can do it now.

SORBS1|SORBS1 is the general protein level. It's detected independent of the phospho-levels. Theoretically, it should include all the phosphoproteins. @pambot please correct me if I am wrong.

[pieterlukasse]

@jjgao thanks for the comments. I also think it would be nice to have SORBS1_pT72 (and others) appear as options when filling in SORBS1. This could probably be done by tweaking the way the gene_alias table is used now in the query page. The only problem could be that you will get a long list of options for each and every gene you fill in the query box....so maybe we need a new feature for this scenario?

[pieterlukasse]

@jjgao will phosphoproteins move to the generic assay feature as well?

[jjgao]

@pieterlukasse yes, that's the plan.